StatAlign: An Extendable Software Package for Joint Bayesian Estimation of Alignments and Evolutionary Trees. Export

@article{citeulike:3188518, abstract = {MOTIVATION: Bayesian analysis is one of the most popular methods in phylogenetic inference. The most commonly used methods fix a single multiple alignment and consider only substitutions as phylogenetically informative mutations, though alignments and phylogenies should be inferred jointly as insertions and deletions also carry informative signals. Methods addressing these issues have been developed only recently and there has not been so far a userfriendly program with a graphical interface that implements these methods. RESULTS: We have developed an extendable software package in the Java programming language that samples from the joint posterior distribution of phylogenies, alignments and evolutionary parameters by applying the Markov chain Monte Carlo method. The package also offers tools for efficient on-the-fly summarisation of the results. It has a graphical interface to configure, start and supervise the analysis, to track the status of the Markov chain and to save the results. The background model for insertions and deletions can be combined with any substitution model. It is easy to add new substitution models to the software package as plugins. The samples from the Markov chain can be summarised in several ways, and new postprocessing plugins may also be installed. AVAILABILITY: The code is available from http://phylogeny-cafe.elte.hu/StatAlign/ CONTACT: miklosi@ramet.elte.hu.}, address = {Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG Oxford, UK.}, author = {Nov\'{a}k, Ad\'{a}m and Mikl\'{o}s, Istv\'{a}n and Lyngs{\o}, Rune and Hein, Jotun}, citeulike-article-id = {3188518}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btn457}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/20/2403}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18753153}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18753153}, day = {27}, doi = {10.1093/bioinformatics/btn457}, issn = {1460-2059}, journal = {Bioinformatics (Oxford, England)}, keywords = {alignment, bayesian, software, statistical-alignment}, month = {August}, posted-at = {2008-11-24 17:56:52}, priority = {2}, title = {StatAlign: An Extendable Software Package for Joint Bayesian Estimation of Alignments and Evolutionary Trees.}, url = {http://dx.doi.org/10.1093/bioinformatics/btn457}, year = {2008} }

TY - JOUR ID - citeulike:3188518 L3 - citeulike-article-id:3188518 N2 - MOTIVATION: Bayesian analysis is one of the most popular methods in phylogenetic inference. The most commonly used methods fix a single multiple alignment and consider only substitutions as phylogenetically informative mutations, though alignments and phylogenies should be inferred jointly as insertions and deletions also carry informative signals. Methods addressing these issues have been developed only recently and there has not been so far a userfriendly program with a graphical interface that implements these methods. RESULTS: We have developed an extendable software package in the Java programming language that samples from the joint posterior distribution of phylogenies, alignments and evolutionary parameters by applying the Markov chain Monte Carlo method. The package also offers tools for efficient on-the-fly summarisation of the results. It has a graphical interface to configure, start and supervise the analysis, to track the status of the Markov chain and to save the results. The background model for insertions and deletions can be combined with any substitution model. It is easy to add new substitution models to the software package as plugins. The samples from the Markov chain can be summarised in several ways, and new postprocessing plugins may also be installed. AVAILABILITY: The code is available from http://phylogeny-cafe.elte.hu/StatAlign/ CONTACT: miklosi@ramet.elte.hu. JF - Bioinformatics (Oxford, England) SN - 1460-2059 AD - Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG Oxford, UK. TI - StatAlign: An Extendable Software Package for Joint Bayesian Estimation of Alignments and Evolutionary Trees. KW - alignment KW - bayesian KW - software KW - statistical-alignment AU - Novák, Adám AU - Miklós, István AU - Lyngsø, Rune AU - Hein, Jotun PY - 2008/08/27/ UR - http://dx.doi.org/10.1093/bioinformatics/btn457 ER -